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Vaccine Ontology (VO) User Cases and Groups

     We have already formed many user cases that uses VO to address specific scientific questions. These VO user cases are being studied by many research groups around the world. For example, a group of professors in the University of Michigan has formed the University of Michigan Vaccine Informatics and Resource Advisory Committee (VIRAC). Many researchers in the VIRAC have started to use VO in their vaccine specific research. Many groups in the USA and around the world have also started to apply VO to various user cases. The following is a list of the VO user cases implemented by different research groups:

1. VO-based Natural Lanuge Processing (NLP): Ontology-based NLP allows more accurate performance on literature mining. VIOLIN is collaborating with the National Center for Integrative Biomedical Informatics (NCIBI) led by Drs. Brian Athey and Gil Omenn to develop VO-based NLP tool to enhance vaccine literature mining. Our focused infectious disease models are Brucella and E. coli:
   • Dr. Oliver He's lab is analyzing the interactions between host and Brucella vaccines. Dr. He is interested in using the VO to study differential immune responses induced by Brucella vaaccines (e.g., RB51 and Strain 19) in various hosts (e.g., human, cattle, and mouse).
   • Dr. Harry Mobley's lab is developing subunit vaccines against urinary tract infection (UTI) caused by uropathogenic Escherichia coli (UPEC) using reverse vaccinology. Dr. Mobley is interested in applying the VO for vaccine target prediction and study of immune mechansim and potential pathogenesis of protective antigens.
2. VO-based Immune Response Network: VIOLIN is working with NCIBI to develop a VO-based immune response network system for study of protective immune responses against infectious diseases. Brucella (domain expert: Dr. Oliver He) and E. coli (domain expert: Dr. Harry Mobley) have been chosen as user cases for this system development.
3. Vaccine Semantic Web: Simply speaking, the Semantic Web is a way to make computers understand computers. Ontologies are the foundations for the Semantic Web. VIOLIN is collabarating with Alan Ruttenberg from Science Commons to develop a vaccine-oriented Semantic Web system using VO and other ontologies.
4. Integration of VO with OBI: Many VO terms (e.g., vaccination) are related to various vaccine experiments that may be the coverage domains of the Ontology for Biomedical Investigations (OBI). Vaccine research has provided user case studies for OBI development. Many members in the VO team are also part of the OBI Consortium (e.g., Dr. Bjeorn Peters, Dr. Richard Scheuermann, and Alan Ruttenberg). We will ensure synergistic development of VO and OBI.
5. Application of VO in Epitope-related Modeling: Immune dominant epitopes are critical for vaccine development. Dr. Bjoern Peters (La Jolla Institute for Allergy and Immunology), the bioinformatics leader of the Immune Epitope Database project (http://www.immuneepitope.org), is interested in using VO for epitope/immunology related computational modeling.
6. Application of VO in modeling laboratory animal models used in vaccine research: A group of researchers, including Drs. Lesley Colby, Howard Rush, and Thomas Todd, in the Unit for Lab Animal Medicine of the University of Michigan Medical School are interested in applying VO to model the laboratory animal models used in vaccine research.
7. Application of VO in Developtment of Influenza Ontology (InfluenzO): InfluenzO is an influenza application ontology that references more than 10 other ontologies. Dr. Richard Scheuermann (University of Texas Southwestern Medical Center), a member of the InfluenzO Consortium, is interested in applying VO in InfluenzO.
8. Application of VO in Canadian Flu Pandemic Preparedness Network: We are collaborating with a group of Canadian scientists including Dr. Ryan Brinkman to apply VO in a collaborative project with an aim to develop a Canadian Flu Pandemic Preparedness network.
9. Application of VO in tuberculosis vaccine research: Dr. Zhenhua Yang's lab is studying DNA polymorphisms in genes used for TB vaccine development (e.g., pepA and PPE18) among clinical strains of Mycobacterium tuberculosis (See reference: PMID: 17893137). Dr. Yang is interested in using the VO to organize and analyze vaccine gene polymorphisms.

     We welcome more users to join our VO user groups with more VO-based case studies and examples.